Boxbe is one that I have encountered people using: http://www.boxbe.com/help It's a little surprising this was never a standard part of email. It's the same workflow as granting permission to be contacted by IM.
Based on a quick search, you are right that the phrase "permission based email" has been SEO'ed into uselessness by email marketing services. What should it be called? Screening? But the spam filtering services have almost SEO'ed that into uselessness.
Boxbe is an interesting service, thanks. Maybe this 'permission-based' was never a standard because spam didn't exist back then and, later when it did exist, didn't play well with the idea of mailing lists. In the latter context it's funny how this search term is SEO'd to return marketing services!
Having just read a former google abuse team member's take on end to end encryption and anti-spam[1], this topic now looks a lot more complex. Regarding IM's, he mentions how spam-free WhatsApp is and argues that spam is a lot easier to fight when you have central control because you can change anything at any time at any point (client or server).
IM is low in spam because spammers would have to wheedle their way onto your contact list to spam you. Same for social networks. You just delete or block spammy "friends."
Based on a quick search, you are right that the phrase "permission based email" has been SEO'ed into uselessness by email marketing services. What should it be called? Screening? But the spam filtering services have almost SEO'ed that into uselessness.